correct documentation

DESCRIPTION

@@ -2,7 +2,7 @@ Package: leiden
 Type: Package
 Title: R Implementation of Leiden Clustering Algorithm
 Version: 0.3.3
-Date: 2020-01-17
+Date: 2020-02-03
 Authors@R: c(person("S. Thomas", "Kelly", email = "tom.kelly@riken.jp", role = c("aut", "cre", "trl")),
            person("Vincent A.", "Traag", email = "v.a.traag@cwts.leidenuniv.nl", role = c("com")))
 Description: Implements the 'Python leidenalg' module to be called in R.

NEWS.md

@@ -1,3 +1,9 @@
+# leiden 0.3.3
+
+* bug fixes for documentation in response to changes to R
+
+see development version: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16223
+
 # leiden 0.3.2
 
 * added support for passing weighted igraph objects

R/leiden.R

@@ -7,7 +7,6 @@
 ##' @param resolution_parameter A parameter controlling the coarseness of the clusters
 ##' @param seed Seed for the random number generator. By default uses a random seed if nothing is specified.
 ##' @param n_iterations Number of iterations to run the Leiden algorithm. By default, 2 iterations are run. If the number of iterations is negative, the Leiden algorithm is run until an iteration in which there was no improvement.
-##' @param ... 	Arguments to be passed to methods
 ##' @return A partition of clusters as a vector of integers
 ##' @examples
 ##' #check if python is availble

README.md

@@ -1,6 +1,6 @@
 # Leiden Algorithm
 
-## leiden version 0.3.2
+## leiden version 0.3.3
 
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/leiden)](https://cran.r-project.org/package=leiden)
 [![Travis Build Status](https://travis-ci.org/TomKellyGenetics/leiden.svg?branch=master)](https://travis-ci.org/TomKellyGenetics/leiden)
@@ -274,15 +274,15 @@ Please cite this implementation R in if you use it:
 To cite the leiden package in publications use:
 
   S. Thomas Kelly (2019). leiden: R implementation of the Leiden algorithm. R
-  package version 0.3.2 https://github.com/TomKellyGenetics/leiden
+  package version 0.3.3 https://github.com/TomKellyGenetics/leiden
 
 A BibTeX entry for LaTeX users is
 
   @Manual{,
     title = {leiden: R implementation of the Leiden algorithm},
     author = {S. Thomas Kelly},
     year = {2018},
-    note = {R package version 0.3.2},
+    note = {R package version 0.3.3},
     url = {https://github.com/TomKellyGenetics/leiden},
   }
  ```

cran-comments.md

@@ -12,9 +12,9 @@
 
 ## Updates
 
-Minor update to include support for weighted igraph objects.
+Minor update to include resolve issues with documentation on development version of R.
 
-This release is compatible with proposed changes to the Seurat (v3.1.2) package. This version will be a dependency of Seurat. This version of Seurat is not available for checking with revdep but has been checked locally after installing the develop version from GitHub.
+See development version: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16223
 
 ## Python integration
 

inst/CITATION

@@ -4,11 +4,11 @@ citEntry(entry = "Manual",
          title        = "leiden: R implementation of the Leiden algorithm",
          author       = personList(as.person("S. Thomas Kelly")),
          year         = "2019",
-         note         = "R package version 0.3.2",
+         note         = "R package version 0.3.3",
          url          = "https://github.com/TomKellyGenetics/leiden",
 
          textVersion  =
-           paste("S. Thomas Kelly (2019). leiden: R implementation of the Leiden algorithm. R package version 0.3.2",
+           paste("S. Thomas Kelly (2019). leiden: R implementation of the Leiden algorithm. R package version 0.3.3",
                  "https://github.com/TomKellyGenetics/leiden")
 )